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<h2>Option: separate</h2>

<h4>Syntax</h4>

<p><code>-separate &#60;distance&#62; &#60;shift&#62;</code></p>


<h4>Description</h4>

<p>This option separates atoms that are too close to one another.</p>

<p>When two atoms are found closer than the specified &#60;distance&#62;, they are both pulled apart from each other by the given &#60;shift&#62;. The direction of the shift is along the vector joining the two atoms.</p>

<p>If the two atoms share exactly the same position (i.e. if their joining vector has a naught length), then the two atoms are moved along the Cartesian vector [1,1,1] (note that this has nothing to do with the crystal orientation).</p>

<p>The comparison of distances is based only on cores. If shells are present, both core and shell are moved by the same vector.</p>

<p>If a selection was defined (with the <a href="./option_select.html">option <code>-select</code></a>) then the neighbor search is performed on all atoms, but only selected atoms are shifted.</p>



<h4>Default</h4>

<p>By default atoms are not separated.</p>



<h4>Examples</h4>

<ul>
<li><code class="command">atomsk initial.cfg -separate 0.5 0.2 final.xyz</code>
<p>This will detect atoms that are closer than 0.5 &Aring;, and move each of them by 0.2 &Aring; apart from the other.</p></li>
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